Investigating the Relationship between CRISPR-Cas Content and Growth Rate in Bacteria.

CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large data set of 4,142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number, Cas gene cluster number, and Cas gene number. Different data sets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages. IMPORTANCE Accumulating evidence indicates that slowing the growth of cultured bacteria could stimulate their CRISPR spacer acquisition. We observed a positive correlation between CRISPR-Cas content and cell cycle duration across the bacteria domain. This observation extends the physiological conclusion to an evolutionary one. In addition, the correlation provides evidence supporting the existence of a trade-off between bacterial growth/reproduction and antiviral resistance.

Gastric Cancer Screening Methods: A Comparative Study of the Chinese New Gastric Cancer Screening Score and Kyoto Classification of Gastritis.

Objective: To evaluate the Chinese new gastric cancer screening score (i.e., Li's score) and Kyoto Classification of Gastritis for screening gastric cancer. Methods: A total of 702 patients were scored using the two scoring methods. Gastric atrophy, intestinal metaplasia, and gastric cancer (including early gastric cancer) were compared between the two scoring methods. The area under the ROC curve, sensitivity, and specificity of the two scoring methods were evaluated. Results: Both of the two scoring methods found that gastric atrophy, intestinal metaplasia, and gastric cancer (including early gastric cancer) were all significantly higher in the medium-risk and high-risk group patients than those in the low-risk group patients. According to the Kyoto Classification of Gastritis, patients in the high-risk group had more gastric atrophy, intestinal metaplasia, and gastric cancer than those in the medium-risk group patients. Gastric atrophy, intestinal metaplasia, and gastric cancer in the low-risk and medium-risk group patients evaluated by the Li score were all significantly higher than those in patients with corresponding risk level evaluated by Kyoto Classification of Gastritis, respectively. The area under the ROC curve of the Li score was 0.702, and the sensitivity and specificity were 57.6% and 85.3%, respectively. The area under the ROC curve of the Kyoto Classification of Gastritis was 0.826, and the sensitivity and specificity were 75.4% and 83.6%, respectively. Conclusion: Both Li's score and Kyoto Classification of Gastritis showed good screening value for gastric cancer, but Kyoto Classification of Gastritis was more sensitive than the Li score.

Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C.

Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. We observed an abrupt increase of bacterial CRISPR-Cas abundance at around 45°C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45°C. From the literature, we noticed that the diversities of cellular predators (like protozoa, nematodes, and myxobacteria) have a steep decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45°C and almost disappears above 60°C. We propose that viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority at higher temperatures. In temperature ranges where the abundance of cellular predators does not change with temperature, the growth temperatures of bacteria would not significantly affect their CRISPR-Cas contents. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.

A positive correlation between GC content and growth temperature in prokaryotes.

BACKGROUND: GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. RESULTS: With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. CONCLUSIONS: This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

High-Performance Evolution of Ni2P@Hierarchical HZSM-5 as the Guaiacol Hydrodeoxygenation Catalyst.

Hydrodeoxygenation (HDO) is one of the effective methods to upgrade biomass pyrolysis oil, but the development of a low-cost, high-performance HDO catalyst still faces enormous challenges. In this work, a facile and eco-friendly approach is developed to synthesize the Ni2P@hierarchical HZSM-5 catalyst. Structure and acidity of the catalyst can be controlled by simply adjusting the proportions of ammonia solution and the silicon to aluminum ratio, which are closely related to the performance of the catalyst. Experimental results reveal that the Ni2P@hierarchical HZSM-5 catalyst with Si/Al = 85 under NH3·H2O/Ni = 14 exhibits the highest activity of 98% guaiacol conversion, along with a 78.8% yield of cyclohexane (reaction conditions: 300 °C, 3 MPa H2). In addition, the guaiacol reaction network is provided.

A novel multiplex xMAP assay for generic detection of avian, fish, and ruminant DNA in feed and feedstuffs.

The identification of animal species in feed and feedstuffs is important for detecting contamination and fraudulent replacement of animal components that might cause health and economic problems. A novel multiplex assay, based on xMAP technology and the generic detection of closely related species, was developed for the simultaneous differential detection of avian, fish, and ruminant DNA in products. Universal primers and probes specific to avian, fish, or ruminant species were designed to target a conserved mitochondrial DNA sequence in the 12S ribosomal RNA gene (rRNA). The assay specificity was validated using samples of 27 target and 10 nontarget animal species. The limits of detection of the purified DNA were determined to be 0.2 pg/µL-0.1 ng/µL by testing the meat samples of six species and four feedstuffs. The detection sensitivity of the experimental mixtures was demonstrated to be 0.01% (weight percentage). The assay's suitability for practical application was evaluated by testing feed samples; unlabeled animal ingredients were detected in 32% of the 56 samples. The assay differentially detected the three targeted categories of animal species in less than 2 h, reflecting improvements in speed and efficiency. Based on these results, this novel multiplex xMAP assay provides a reliable and highly efficient technology for the routine detection of animal species in feed and other products for which this information is needed.

Magnetic Resonance Venography Findings of Obstructed Hepatic Veins and the Inferior Vena Cava in Patients with Budd-Chiari Syndrome.

Objective: This study aimed to illustrate the magnetic resonance venography (MRV) manifestations of obstructed hepatic veins (HVs), the inferior vena cava (IVC), and accessory hepatic veins (AHVs) in patients with Budd-Chiari syndrome (BCS) and to evaluate the visualization capacity of MRV in the diagnosis of BCS. Materials and Methods: Fifty-two patients with chronic BCS were included in this study. All patients were examined via MRV performed with a 3T system following injections of gadolinium-diethylene triamine pentaacetic acid (Gd-DTPA) or Gd-ethoxibenzyl-DTPA. HV and IVC lesions were classified, and their characteristics were described. HV cord-like occlusions detected via MRV were compared using ultrasonography (US). Digital subtraction angiography (DSA) was performed as a contrast in the MRV detection of IVC lesions. The HVs draining collaterals, mainly AHVs, were carefully observed. HV lesions were classified as segmental stenosis, segmental occlusion, membranous stenosis, membranous occlusion, cord-like occlusion, or non-visualized. Except for patent IVCs, IVC lesions were classified as segmental occlusion, segmental stenosis, membranous occlusion, membranous stenosis, and hepatomegaly-induced stenosis. Results: All patients (52/52, 100%) showed HV lesions of different degrees. MRV was inferior to US in detecting cord-like occlusions (6 vs. 19, χ2 = 11.077, p < 0.001). Dilated AHVs, including 50 (50/52, 96.2%) caudate lobe veins and 37 (37/52, 71.2%) inferior HV and AHV lesions, were well-detected. There were no significant differences in detecting segmental lesions and thrombosis between MRV and DSA (χ2 = 0.000, p1 = 1.000, p2 = 1.000). The capacity of MRV to detect membranous lesions was inferior to that of DSA (7 vs. 15, χ2 = 6.125, p = 0.013). Conclusion: In patients with BCS, MRV can clearly display the lesions in HVs and the IVC, as well as in AHVs, and it has diagnostic and therapeutic value.

Association of interleukin 22 polymorphisms with gastric cancer risk.

Interleukin (IL)-22 has been implicated in inflammation and tumorigenesis. To date, no studies have investigated the role of IL-22 polymorphism in the carcinogenesis of gastric cancer (GC). In this study, we aimed to investigate the association of IL-22 polymorphisms with the risk of GC in a Chinese population. One hundred eight GC patients and 110 healthy controls were included in the study. IL-22 rs1179251, rs2227485, and rs2227473 polymorphisms were determined by PCR amplification and DNA sequencing. Haplotypes were constructed, and a possible association of these haplotypes with GC was assessed. The distribution of IL-22 rs1179251 polymorphism with clinical parameters was also analyzed. The IL-22 rs1179251 polymorphism was significantly associated with an increased risk of GC (p < 0.05). Stratified analysis revealed that rs1179251 was associated with advanced stages, lymph node metastases, and distant metastases of GC (p < 0.05). No associations were found between rs2227485 and rs2227473 and the risk of GC (p > 0.05). Three possible haplotypes (C(rs1179251)-C(rs2227485)-G(rs2227485), C(rs1179251)-T(rs2227485)-G(rs2227485), and G(rs1179251)-T(rs2227485)-A(rs2227485)) were identified, but no associations were found between these and the risk of GC (p > 0.05). In summary, our study demonstrates that the rs1179251 polymorphism of IL-22 was associated with an increased risk of GC and may influence the progression of GC. Future larger studies with other ethnic populations are required to confirm these findings.

Combination of multiplex PCR with denaturing high-performance liquid chromatography for rapid detection of Mycobacterium genus and simultaneous identification of the Mycobacterium tuberculosis complex.

A new assay with the combination of multiplex polymerase chain reaction and denaturing high-performance liquid chromatography analysis was developed for simultaneous detection of Mycobacterium genus and identification of the Mycobacterium tuberculosis complex (MTC). Targeting at genus-specific 16S rRNA sequence of Mycobacterium and specific insertion elements IS6110 and IS1081 of MTC, the assay was validated with 84 strains covering 23 mycobacteria species and 30 strains of non-mycobacteria species. No cross reactivity was observed. Clinical application was carried out on 198 specimens (155 human sputum and 43 bovine tissue samples) and compared with culture. The multiplex assay detected all culture-positive (36 in number) and 35.2% (57/162) culture-negative specimens. The molecular assay was fast that could be completed within 1 h on purified DNA, with the limit of detection as 0.8-1.6 pg per reaction on DNA template. This work provided a useful laboratory tool for rapid identification of Mycobacterium and differentiation of MTC and nontuberculous mycobacteria.

Preoperative demonstration of neurovascular relationship in trigeminal neuralgia by using 3D FIESTA sequence.

PURPOSE: The purpose of the study was to evaluate the value of high-resolution three-dimensional fast imaging employing steady-state acquisition (3D FIESTA) imaging in the visualization of neurovascular relationship in patients with trigeminal neuralgia (TN). METHODS: Thirty-seven patients with unilateral typical TN underwent 3D FIESTA imaging. Neurovascular relationship at the trigeminal root entry zone was reviewed by an experienced neuroradiologist, who was blinded to the clinical details. The imaging results were compared with the operative findings in all patients. RESULTS: In 37 patients with TN, 3D FIESTA imaging identified surgically verified neurovascular contact in 35 of 36 symptomatic nerves. Based on surgical findings, the sensitivity and specificity of magnetic resonance (MR) imaging were 97.2% and 100%, respectively. Agreement between the position (medial, lateral, superior and inferior) of the compressing vessel relative to the trigeminal nerve identified by MR imaging and surgery was excellent (K=0.81; 95% confidence interval, 0.56-1.00). A statistically significant difference was found between the site of neurovascular contact and the clinical symptom related to the trigeminal branch (Fisher's Exact Test, P<.001). CONCLUSIONS: Use of 3D FIESTA sequence enables accurate visualization of neurovascular contact in patients with TN. Anatomic relationships defined by this method can be useful in surgical planning and predicting surgical findings.